fix: process data doesn't allow bad formatted

stratigraphic order

Author: Lachlan Grose

LoopStructural/modelling/input/process_data.py

@@ -60,8 +60,8 @@ def __init__(   self,
         The processor will generate the best possible data set given the input data. If you only want to build a fault 
         network then only fault locations, orientations edges and properties are required
         """
-        
-        self._stratigraphic_order = stratigraphic_order
+        self._stratigraphic_order = None
+        self.stratigraphic_order = stratigraphic_order
         self._thicknesses = thicknesses
         self._use_thickness = use_thickness
         if self.thicknesses is None:
@@ -85,7 +85,8 @@ def __init__(   self,
         self._fault_properties = None
         self.fault_properties = fault_properties
         self._fault_network = None
-        self.set_fault_network(fault_edges,fault_edge_properties)# = fault_graph
+        if fault_edges is not None and fault_edge_properties is not None:
+            self.set_fault_network(fault_edges,fault_edge_properties)# = fault_graph
         self._fault_stratigraphy = fault_stratigraphy
         self._intrusions = intrusions
         self._thicknesses = thicknesses
@@ -96,7 +97,21 @@ def __init__(   self,
         self._foliation_properties = {} #empty dictionary of foliation parameters
         self.foliation_properties = None
 
+    @property
+    def stratigraphic_order(self):
+        return self._stratigraphic_order
 
+    @stratigraphic_order.setter
+    def stratigraphic_order(self, stratigraphic_order):
+        if isinstance(stratigraphic_order[0][1],list) == False:
+            raise TypeError('Stratigraphic_order must of the format [[(\'group_name\',[\'unit1\',\'unit2\']),(\'group_name2\',[\'unit3\',\'unit4\'])]]')
+        if isinstance(stratigraphic_order,list) == False:
+            raise TypeError('Stratigraphic_order must be a list')
+        if isinstance(stratigraphic_order[0][1][0],str) == False:
+            raise TypeError('Stratigraphic_order elements must be strings')
+        self._stratigraphic_order = stratigraphic_order
+
+
     @property
     def colours(self):
         return self._colours
@@ -119,10 +134,12 @@ def stratigraphic_column(self):
         for name, sg in self._stratigraphic_order:
             stratigraphic_column[name] = {}
             for g in reversed(sg):
-                stratigraphic_column[name][g] = {'max': val[g]+self.thicknesses[g], 'min': val[g] , 'id': unit_id, 'colour':self.colours[g]}
+                if g in self.thicknesses:
+                    stratigraphic_column[name][g] = {'max': val[g]+self.thicknesses[g], 'min': val[g] , 'id': unit_id, 'colour':self.colours[g]}
                 unit_id += 1
         # add faults into the column 
-        stratigraphic_column['faults'] = self.fault_properties.to_dict('index')
+        if self.fault_properties is not None:
+            stratigraphic_column['faults'] = self.fault_properties.to_dict('index')
         return stratigraphic_column
 
 
@@ -280,8 +297,10 @@ def data(self):
         before any of the calculated attributes are accessed
         """
         dataframes = []
-        dataframes.append(self.contacts)
-        dataframes.append(self.contact_orientations)
+        if self.contacts is not None:
+            dataframes.append(self.contacts)
+        if self.contact_orientations is not None:
+            dataframes.append(self.contact_orientations)
         if self.fault_orientations is not None:
             dataframes.append(self.fault_orientations)
         if self.fault_locations is not None:
@@ -310,7 +329,7 @@ def vector_scale(self,vector_scale):
     @property
     def stratigraphic_name(self):
         names = []
-        for sg in self._stratigraphic_order:
+        for name, sg in self._stratigraphic_order:
             for g in sg:
                 names.append(g)
         return names
@@ -330,8 +349,12 @@ def _stratigraphic_value(self):
         for name, sg in self._stratigraphic_order:
             value = 0. #reset for each supergroup
             for g in reversed(sg):
-                stratigraphic_value[g] = value #+ self._thicknesses[g]
-                value+=self._thicknesses[g]
+                if g not in self._thicknesses:
+                    logger.warning('No thicknesses for {}'.format(g))
+                    stratigraphic_value[g] = np.nan
+                else:
+                    stratigraphic_value[g] = value #+ self._thicknesses[g]
+                    value+=self._thicknesses[g]
         return stratigraphic_value
 
     def _update_feature_names(self,dataframe):
@@ -386,6 +409,8 @@ def contacts(self,contacts):
 
     @property
     def contact_orientations(self):
+        if self._contact_orientations is None:
+            return None
         contact_orientations = self._contact_orientations.copy()
         #scale
         contact_orientations.loc[~np.isnan(contact_orientations['nz']),['nx', 'ny', 'nz']]*=self.vector_scale*\

tests/unit_tests/input/test_data_processor.py

@@ -1,20 +1,12 @@
-# from LoopStructural.modelling import ProcessInputData
-# import pandas as pd
-# import numpy as np
+from LoopStructural.modelling import ProcessInputData
+import pandas as pd
+import numpy as np
 
-# contacts - 
-# contacts=None
-# contact_orientations = None
-# stratigraphic_order = None
-# fault_orientations = None 
-# fault_locations = None
-# fault_properties = None 
-# fault_edges = None
-# intrusions = None
-# fault_stratigraphy = None
-# thicknesses = None
-# colours = None
-
-# def test_create_processor():
-#     contacts = np.zeros(
-#     ProcessInputData(
+def test_create_processor():
+    df = pd.DataFrame(np.random.rand(10,3),columns=['X','Y','Z'])
+    df['name'] = ['unit_{}'.format(name%2) for name in range(10)]
+    stratigraphic_order = [('sg',['unit_0','unit_1'])]
+    thicknesses = {'unit_0':1.,'unit_1':0.5}
+    processor = ProcessInputData(contacts=df,stratigraphic_order=stratigraphic_order,thicknesses=thicknesses)
+    assert((processor.data['val'].unique() == np.array([0.5,0])).all())
+    

tests/unit_tests/modelling/test_geological_model.py

@@ -44,5 +44,4 @@ def test_element_number_FDI():
 def test_buffer():
     model = GeologicalModel([0,0,0],[5,5,5],rescale=True)
     interpolator = model.get_interpolator(interpolatortype='FDI',nelements=1e5,buffer=0.2)
-    print(interpolator.support.origin)
     assert np.sum(interpolator.support.origin + .2) == 0